Package: goProfiles

Version: 1.40.0

Command: rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.40.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.40.0.tar.gz

StartedAt: 2018-04-12 00:28:20 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:32:49 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 269.0 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf goProfiles.buildbin-libdir goProfiles.Rcheck && mkdir goProfiles.buildbin-libdir goProfiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goProfiles.buildbin-libdir goProfiles_1.40.0.tar.gz >goProfiles.Rcheck\00install.out 2>&1 && cp goProfiles.Rcheck\00install.out goProfiles-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=goProfiles.buildbin-libdir --install="check:goProfiles-install.out" --force-multiarch --no-vignettes --timings goProfiles_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/goProfiles.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goProfiles/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'goProfiles' version '1.40.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'goProfiles' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chiDisjoint: no visible global function definition for 'var'
chiIntersect: no visible global function definition for 'var'
chiPnP0Correct: no visible global function definition for 'var'
chiRestrict: no visible global function definition for 'var'
equivalentGOProfiles.GOProfileHtest: no visible global function
  definition for 'qnorm'
equivalentGOProfiles.GOProfileHtest: no visible global function
  definition for 'pnorm'
estimProbPrecision: no visible global function definition for 'qnorm'
generate.multinomial: no visible global function definition for
  'rbinom'
internal.compareGOProf: no visible global function definition for
  'pchisq'
internal.compareGOProf: no visible global function definition for
  'qnorm'
internal.enrichProfile: no visible global function definition for
  'fisher.test'
internal.enrichProfile: no visible global function definition for
  'p.adjust'
internal.equivalentGOProf: no visible global function definition for
  'qnorm'
internal.equivalentGOProf: no visible global function definition for
  'pnorm'
internal.fitGOProf: no visible global function definition for 'pchisq'
internal.fitGOProf: no visible global function definition for 'qnorm'
meanICLength: no visible global function definition for 'qnorm'
meanICLength: no visible global function definition for 'sd'
normIntLength: no visible global function definition for 'qnorm'
plcombChisq: no visible global function definition for 'rchisq'
plot1Prof: no visible global function definition for 'rainbow'
plot1Prof: no visible global function definition for 'par'
plot1Prof: no visible global function definition for 'win.graph'
plot2Prof: no visible global function definition for 'par'
plot2Prof: no visible global function definition for 'win.graph'
plotOne: no visible global function definition for 'barplot'
plotOne: no visible global function definition for 'text'
plotOne: no visible global function definition for 'axis'
plotOne: no visible global function definition for 'title'
plotProfiles: no visible global function definition for 'rainbow'
plotTwo: no visible global function definition for 'par'
plotTwo: no visible global function definition for 'barplot'
plotTwo: no visible global function definition for 'text'
plotTwo: no visible global function definition for 'axis'
plotTwo: no visible global function definition for 'title'
qlcombChisq: no visible global function definition for 'quantile'
qlcombChisq: no visible global function definition for 'rchisq'
rlcombChisq: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  axis barplot fisher.test p.adjust par pchisq pnorm qnorm quantile
  rainbow rbinom rchisq sd text title var win.graph
Consider adding
  importFrom("grDevices", "rainbow", "win.graph")
  importFrom("graphics", "axis", "barplot", "par", "text", "title")
  importFrom("stats", "fisher.test", "p.adjust", "pchisq", "pnorm",
             "qnorm", "quantile", "rbinom", "rchisq", "sd", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
compareGeneLists     17.58   0.14   17.81
equivalentGOProfiles 12.61   0.14   12.81
fisherGOProfiles      6.02   0.05    6.06
mergeProfilesLists    5.32   0.08    5.39
plotProfiles          5.12   0.13    5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
compareGeneLists     22.58   0.22   22.79
equivalentGOProfiles 18.30   0.08   18.39
fisherGOProfiles      7.64   0.10    7.75
printProfiles         6.84   0.01    6.86
plotProfiles          6.69   0.05    6.74
mergeProfilesLists    5.37   0.06    5.43
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/goProfiles.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'goProfiles' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'goProfiles'
    finding HTML links ... done
    CD4ids                                  html  
    GOTermsList                             html  
    basicProfile                            html  
    compSummary                             html  
    compareGOProfiles                       html  
    compareGeneLists                        html  
    compareProfilesLists                    html  
    contractedProfile                       html  
    conversionFunctions                     html  
    drosophila                              html  
    equivSummary                            html  
    equivalentGOProfiles                    html  
    expandedLevel                           html  
    expandedProfile                         html  
    fisherGOProfiles                        html  
    fitGOProfile                            html  
    goProfiles-package                      html  
    hugoIds                                 html  
    mergeProfilesLists                      html  
    ngenes                                  html  
    omimIds                                 html  
    plotProfiles                            html  
    printProfiles                           html  
    prostateIds                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'goProfiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goProfiles' as goProfiles_1.40.0.zip
* DONE (goProfiles)
In R CMD INSTALL
In R CMD INSTALL